A script to decouple the components from Bio-Formats

cpp_decoupling

#! /bin/bash

here=$(pwd)

# Initial clone
cd /tmp
rm -rf /tmp/bioformats-cpp || echo "Already cleaned"

# Clone Bio-Formats
git clone https://github.com/openmicroscopy/bioformats.git bioformats-cpp

# Filter branch to keep only the model components
cd bioformats-cpp
PATHS_TO_KEEP="cpp"
git filter-branch -f --index-filter "git rm --ignore-unmatch --cached -qr -- . && git reset -q \$GIT_COMMIT -- $PATHS_TO_KEEP" --prune-empty -- HEAD

# Clean empty commits
tmpfile=`mktemp -t splitgit`
chmod 755 $tmpfile
echo '#!/usr/bin/env ruby
old_parents = gets.chomp.gsub("-p ", " ")
new_parents = old_parents.empty? ? [] : `git show-branch --independent #{old_parents}`.split
puts new_parents.map{|p| "-p " + p}.join(" ")' > $tmpfile
git filter-branch -f --prune-empty --parent-filter $tmpfile HEAD
rm $tmpfile

cppwrap_decoupling

#! /bin/bash

here=$(pwd)

# Initial clone
cd /tmp
# rm -rf /tmp/bioformats || echo "Already cleaned"

# Clone Bio-Formats
# git clone https://github.com/openmicroscopy/bioformats.git bf-cppwrap

# Filter branch to keep only the model components
cd bf-cppwrap
PATHS_TO_KEEP="components/formats-bsd/cppwrap components/formats-bsd/pom.xml  pom.xml .travis.yml"
git filter-branch -f --index-filter "git rm --ignore-unmatch --cached -qr -- . && git reset -q \$GIT_COMMIT -- $PATHS_TO_KEEP" --prune-empty -- HEAD

# Clean empty commits
tmpfile=`mktemp -t splitgit`
chmod 755 $tmpfile
echo '#!/usr/bin/env ruby
old_parents = gets.chomp.gsub("-p ", " ")
new_parents = old_parents.empty? ? [] : `git show-branch --independent #{old_parents}`.split
puts new_parents.map{|p| "-p " + p}.join(" ")' > $tmpfile
git filter-branch -f --prune-empty --parent-filter $tmpfile HEAD
rm $tmpfile

formats-common-diff

diff --git a/.travis.yml b/.travis.yml
index 5c71fde..abb63c1 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,60 +1,16 @@
 language: java
 
+# This (sudo: false) is needed to "run on container-based infrastructure" on
+# which cache: is available
+# http://docs.travis-ci.com/user/workers/container-based-infrastructure/
+sudo: false
+
+# http://docs.travis-ci.com/user/caching/#Arbitrary-directories
+cache:
+  directories:
+  - $HOME/.m2
+
 jdk:
   - oraclejdk8
   - oraclejdk7
   - openjdk6
-
-env:
-  - BUILD=maven
-  - BUILD=cpp
-  - BUILD=cppwrap
-  - BUILD=flake8
-  - BUILD=sphinx
-  - BUILD=ant
-
-matrix:
-  fast_finish: true
-  allow_failures:
-    - env: "BUILD=cppwrap"
-
-before_install:
-  - if [[ $BUILD == 'cpp' ]]; then sudo add-apt-repository -y ppa:kubuntu-ppa/backports; fi
-  - if [[ $BUILD == 'cpp' ]]; then sudo apt-get -qq update; fi
-  - if [[ $BUILD == 'cpp' ]] || [[ $BUILD == 'cppwrap' ]]; then sudo apt-get install -qq cmake; fi
-  - if [[ $BUILD == 'sphinx' ]]; then sudo add-apt-repository -y "deb http://archive.ubuntu.com/ubuntu/ trusty main universe"; fi
-  - if [[ $BUILD == 'cpp' ]]; then sudo add-apt-repository -y ppa:dhor/myway; fi
-  - sudo apt-get -qq update
-  - if [[ $BUILD != 'sphinx' ]]; then sudo apt-get install -qq python-genshi; fi
-  - if [[ $BUILD == 'cpp' ]] || [[ $BUILD == 'cppwrap' ]]; then sudo apt-get install -qq build-essential libboost1.48-all-dev; fi
-  - if [[ $BUILD == 'cpp' ]]; then sudo apt-get install -qq libgtest-dev libxerces-c-dev libtiff4-dev doxygen graphviz graphicsmagick; fi
-  - if [[ $BUILD == 'sphinx' ]] || [[ $BUILD == 'flake8' ]]; then sudo pip install flake8 Sphinx==1.2.3; fi
-  - if [[ $BUILD == 'sphinx' ]]; then sudo apt-get -y install texlive-latex-base texlive-latex-recommended texlive-xetex; fi
-  - if [[ $BUILD == 'sphinx' ]]; then sudo apt-get -y install texlive-latex-extra texlive-fonts-recommended fonts-texgyre; fi
-  - if [[ $BUILD == 'sphinx' ]]; then sudo fc-cache -rsfv; fi
-
-install:
-  - if [[ $BUILD != 'ant' ]] && [[ $BUILD != 'sphinx' ]] && [[ $BUILD != 'flake8' ]]; then git fetch --tags; fi
-  - if [[ $BUILD == 'maven' ]]; then mvn install -DskipTests=true; fi
-
-script:
-  - ./tools/test-build $BUILD
-
-matrix:
-  exclude:
-    - jdk: openjdk6
-      env: BUILD=flake8
-    - jdk: oraclejdk7
-      env: BUILD=flake8
-    - jdk: openjdk6
-      env: BUILD=sphinx
-    - jdk: oraclejdk7
-      env: BUILD=sphinx
-    - jdk: openjdk6
-      env: BUILD=cpp
-    - jdk: oraclejdk7
-      env: BUILD=cpp
-    - jdk: oraclejdk8
-      env: BUILD=cppwrap
-    - jdk: openjdk6
-      env: BUILD=cppwrap
diff --git a/pom.xml b/pom.xml
index d91982f..ef690a8 100644
--- a/pom.xml
+++ b/pom.xml
@@ -16,28 +16,7 @@
   <inceptionYear>2005</inceptionYear>
 
   <modules>
-    <module>components/specification</module>
-    <module>components/forks/jai</module>
-    <module>components/forks/mdbtools</module>
-    <module>components/forks/poi</module>
-    <module>components/forks/turbojpeg</module>
-    <module>components/autogen</module>
-    <module>components/formats-api</module>
-    <module>components/formats-bsd</module>
-    <module>components/formats-gpl</module>
-    <module>components/bundles/bioformats_package</module>
     <module>components/formats-common</module>
-    <module>components/bio-formats-plugins</module>
-    <module>components/bundles/loci-tools</module>
-    <module>components/metakit</module>
-    <module>components/bundles/ome-tools</module>
-    <module>components/ome-jxr</module>
-    <module>components/ome-xml</module>
-    <module>components/bio-formats-tools</module>
-    <module>components/test-suite</module>
-    <module>components/stubs/lwf-stubs</module>
-    <module>components/stubs/mipav</module>
-    <module>components/xsd-fu</module>
   </modules>
 
   <properties>
@@ -136,130 +115,6 @@
         <artifactId>maven-surefire-plugin</artifactId>
       </plugin>
 
-      <plugin>
-        <groupId>org.codehaus.gmaven</groupId>
-        <artifactId>gmaven-plugin</artifactId>
-        <version>1.4</version>
-        <executions>
-          <execution>
-            <phase>initialize</phase>
-            <goals>
-              <goal>execute</goal>
-            </goals>
-            <configuration>
-              <defaults>
-                <default>UNKNOWN</default>
-              </defaults>
-              <source>
-                import java.util.regex.Pattern
-
-                def ant = new AntBuilder()
-                try {
-                  ant.exec(outputproperty:"shortrevision",
-                    failifexecutionfails:"false",
-                    executable: 'git') {
-                      arg(line:"rev-parse --short HEAD")
-                  }
-                }
-                catch (Exception e) { }
-                try {
-                  ant.exec(outputproperty:"revision",
-                    failifexecutionfails:"false",
-                    executable: 'git') {
-                      arg(line:"rev-parse HEAD")
-                  }
-                }
-                catch (Exception e) { }
-
-                try {
-                  ant.exec(outputproperty:"exactTag",
-                    resultproperty:"exactTagRC",
-                    failifexecutionfails:"true",
-                    failonerror:"false",
-                    executable: 'git') {
-                      arg(line:"describe --match=v[0-9]* --exact")
-                  }
-                }
-                catch (Exception e) {
-                  ant.project.properties.exactTagRC = ""
-                  ant.project.properties.exactTag = ""
-                }
-
-                try {
-                  ant.exec(outputproperty:"describe",
-                    failifexecutionfails:"true",
-                    executable: 'git') {
-                      arg(line:"describe --match=v[0-9]*")
-                  }
-                }
-                catch (Exception e) {
-                  ant.project.properties.describe = ""
-                }
-
-                println ant.project.properties.exactTagRC
-                println ant.project.properties.exactTag
-                println ant.project.properties.describe
-
-                if (ant.project.properties.exactTagRC == 0) {
-                  // if we're building from a tag, set the release name
-                  // to be the tag name, minus the leading 'v'
-                  project.properties.release = ant.project.properties.exactTag.substring(1)
-                }
-                else if (ant.project.properties.describe) {
-                  // if we're building within Git, but not from a tag,
-                  // then use the last known tag's number to set a snapshot
-                  // version
-                  try {
-                    def regex = Pattern.compile("v([0-9]+)[.]([0-9]+)[.]([0-9]+)(.*)")
-                    def groups = regex.matcher(ant.project.properties.describe)
-                    groups.matches()
-                    def major = groups.group(1)
-                    def minor = groups.group(2)
-                    def patch = groups.group(3)
-                    project.properties.release = major + "." + minor + "." + patch + "-SNAPSHOT"
-                  }
-                  catch (IllegalStateException e) {
-                    project.properties.release = ""
-                  }
-                }
-                else {
-                  // if we're building outside of Git, set a default
-                  // version number
-                  project.properties.release = project.properties.default
-                }
-                project.properties.shortrevision = ant.project.properties.shortrevision
-                project.properties.revision = ant.project.properties.revision
-
-                if (!project.properties.release) {
-                  // assume this is a source package outside of Git
-                  // there should be a ant/gitversion.xml file with the
-                  // version information used when the package was created
-
-                  def xmlfile = project.properties.get('project.rootdir') + "/ant/gitversion.xml"
-
-                  def xml = new XmlParser().parse(xmlfile)
-                  for (property in xml.property) {
-                    println "parsing " + property.'@name'
-                    if ('release.version' == property.'@name') {
-                      project.properties.release = property.'@value'
-                    }
-                    else if ('vcs.revision' == property.'@name') {
-                      project.properties.revision = property.'@value'
-                    }
-                    else if ('vcs.shortrevision' == property.'@name') {
-                      project.properties.shortrevision = property.'@value'
-                    }
-                  }
-                }
-
-                println "shortrevision = " + project.properties.shortrevision
-                println "revision = " + project.properties.revision
-                println "release = " + project.properties.release
-              </source>
-            </configuration>
-          </execution>
-        </executions>
-      </plugin>
 
       <!-- Add Implementation-Build entry to JAR manifest. -->
       <plugin>

formats-common_decoupling

#! /bin/bash

here=$(pwd)

# Initial clone
cd /tmp
rm -rf /tmp/formats-common || echo "Already cleaned"

# Clone Bio-Formats
git clone https://github.com/openmicroscopy/bioformats.git formats-common

# Filter branch to keep only the common components
cd formats-common
PATHS_TO_KEEP="components/formats-common pom.xml .travis.yml"
git filter-branch -f --index-filter "git rm --ignore-unmatch --cached -qr -- . && git reset -q \$GIT_COMMIT -- $PATHS_TO_KEEP" --prune-empty -- HEAD

# Clean empty commits
tmpfile=`mktemp -t splitgit`
chmod 755 $tmpfile
echo '#!/usr/bin/env ruby
old_parents = gets.chomp.gsub("-p ", " ")
new_parents = old_parents.empty? ? [] : `git show-branch --independent #{old_parents}`.split
puts new_parents.map{|p| "-p " + p}.join(" ")' > $tmpfile
git filter-branch -f --prune-empty --parent-filter $tmpfile HEAD
rm $tmpfile


# Apply git diff to let Travis compile
git apply $here/ome-model-diff

ome-model-diff

diff --git a/.travis.yml b/.travis.yml
index 5c71fde..abb63c1 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,60 +1,16 @@
 language: java
 
+# This (sudo: false) is needed to "run on container-based infrastructure" on
+# which cache: is available
+# http://docs.travis-ci.com/user/workers/container-based-infrastructure/
+sudo: false
+
+# http://docs.travis-ci.com/user/caching/#Arbitrary-directories
+cache:
+  directories:
+  - $HOME/.m2
+
 jdk:
   - oraclejdk8
   - oraclejdk7
   - openjdk6
-
-env:
-  - BUILD=maven
-  - BUILD=cpp
-  - BUILD=cppwrap
-  - BUILD=flake8
-  - BUILD=sphinx
-  - BUILD=ant
-
-matrix:
-  fast_finish: true
-  allow_failures:
-    - env: "BUILD=cppwrap"
-
-before_install:
-  - if [[ $BUILD == 'cpp' ]]; then sudo add-apt-repository -y ppa:kubuntu-ppa/backports; fi
-  - if [[ $BUILD == 'cpp' ]]; then sudo apt-get -qq update; fi
-  - if [[ $BUILD == 'cpp' ]] || [[ $BUILD == 'cppwrap' ]]; then sudo apt-get install -qq cmake; fi
-  - if [[ $BUILD == 'sphinx' ]]; then sudo add-apt-repository -y "deb http://archive.ubuntu.com/ubuntu/ trusty main universe"; fi
-  - if [[ $BUILD == 'cpp' ]]; then sudo add-apt-repository -y ppa:dhor/myway; fi
-  - sudo apt-get -qq update
-  - if [[ $BUILD != 'sphinx' ]]; then sudo apt-get install -qq python-genshi; fi
-  - if [[ $BUILD == 'cpp' ]] || [[ $BUILD == 'cppwrap' ]]; then sudo apt-get install -qq build-essential libboost1.48-all-dev; fi
-  - if [[ $BUILD == 'cpp' ]]; then sudo apt-get install -qq libgtest-dev libxerces-c-dev libtiff4-dev doxygen graphviz graphicsmagick; fi
-  - if [[ $BUILD == 'sphinx' ]] || [[ $BUILD == 'flake8' ]]; then sudo pip install flake8 Sphinx==1.2.3; fi
-  - if [[ $BUILD == 'sphinx' ]]; then sudo apt-get -y install texlive-latex-base texlive-latex-recommended texlive-xetex; fi
-  - if [[ $BUILD == 'sphinx' ]]; then sudo apt-get -y install texlive-latex-extra texlive-fonts-recommended fonts-texgyre; fi
-  - if [[ $BUILD == 'sphinx' ]]; then sudo fc-cache -rsfv; fi
-
-install:
-  - if [[ $BUILD != 'ant' ]] && [[ $BUILD != 'sphinx' ]] && [[ $BUILD != 'flake8' ]]; then git fetch --tags; fi
-  - if [[ $BUILD == 'maven' ]]; then mvn install -DskipTests=true; fi
-
-script:
-  - ./tools/test-build $BUILD
-
-matrix:
-  exclude:
-    - jdk: openjdk6
-      env: BUILD=flake8
-    - jdk: oraclejdk7
-      env: BUILD=flake8
-    - jdk: openjdk6
-      env: BUILD=sphinx
-    - jdk: oraclejdk7
-      env: BUILD=sphinx
-    - jdk: openjdk6
-      env: BUILD=cpp
-    - jdk: oraclejdk7
-      env: BUILD=cpp
-    - jdk: oraclejdk8
-      env: BUILD=cppwrap
-    - jdk: openjdk6
-      env: BUILD=cppwrap
diff --git a/pom.xml b/pom.xml
index 07ba51e..38302d5 100644
--- a/pom.xml
+++ b/pom.xml
@@ -17,26 +17,7 @@
 
   <modules>
     <module>components/specification</module>
-    <module>components/forks/jai</module>
-    <module>components/forks/mdbtools</module>
-    <module>components/forks/poi</module>
-    <module>components/forks/turbojpeg</module>
-    <module>components/autogen</module>
-    <module>components/formats-api</module>
-    <module>components/formats-bsd</module>
-    <module>components/formats-gpl</module>
-    <module>components/bundles/bioformats_package</module>
-    <module>components/formats-common</module>
-    <module>components/bio-formats-plugins</module>
-    <module>components/bundles/loci-tools</module>
-    <module>components/metakit</module>
-    <module>components/bundles/ome-tools</module>
-    <module>components/ome-jxr</module>
     <module>components/ome-xml</module>
-    <module>components/bio-formats-tools</module>
-    <module>components/test-suite</module>
-    <module>components/stubs/lwf-stubs</module>
-    <module>components/stubs/mipav</module>
     <module>components/xsd-fu</module>
   </modules>
 
@@ -136,130 +117,6 @@
         <artifactId>maven-surefire-plugin</artifactId>
       </plugin>
 
-      <plugin>
-        <groupId>org.codehaus.gmaven</groupId>
-        <artifactId>gmaven-plugin</artifactId>
-        <version>1.4</version>
-        <executions>
-          <execution>
-            <phase>initialize</phase>
-            <goals>
-              <goal>execute</goal>
-            </goals>
-            <configuration>
-              <defaults>
-                <default>UNKNOWN</default>
-              </defaults>
-              <source>
-                import java.util.regex.Pattern
-
-                def ant = new AntBuilder()
-                try {
-                  ant.exec(outputproperty:"shortrevision",
-                    failifexecutionfails:"false",
-                    executable: 'git') {
-                      arg(line:"rev-parse --short HEAD")
-                  }
-                }
-                catch (Exception e) { }
-                try {
-                  ant.exec(outputproperty:"revision",
-                    failifexecutionfails:"false",
-                    executable: 'git') {
-                      arg(line:"rev-parse HEAD")
-                  }
-                }
-                catch (Exception e) { }
-
-                try {
-                  ant.exec(outputproperty:"exactTag",
-                    resultproperty:"exactTagRC",
-                    failifexecutionfails:"true",
-                    failonerror:"false",
-                    executable: 'git') {
-                      arg(line:"describe --match=v[0-9]* --exact")
-                  }
-                }
-                catch (Exception e) {
-                  ant.project.properties.exactTagRC = ""
-                  ant.project.properties.exactTag = ""
-                }
-
-                try {
-                  ant.exec(outputproperty:"describe",
-                    failifexecutionfails:"true",
-                    executable: 'git') {
-                      arg(line:"describe --match=v[0-9]*")
-                  }
-                }
-                catch (Exception e) {
-                  ant.project.properties.describe = ""
-                }
-
-                println ant.project.properties.exactTagRC
-                println ant.project.properties.exactTag
-                println ant.project.properties.describe
-
-                if (ant.project.properties.exactTagRC == 0) {
-                  // if we're building from a tag, set the release name
-                  // to be the tag name, minus the leading 'v'
-                  project.properties.release = ant.project.properties.exactTag.substring(1)
-                }
-                else if (ant.project.properties.describe) {
-                  // if we're building within Git, but not from a tag,
-                  // then use the last known tag's number to set a snapshot
-                  // version
-                  try {
-                    def regex = Pattern.compile("v([0-9]+)[.]([0-9]+)[.]([0-9]+)(.*)")
-                    def groups = regex.matcher(ant.project.properties.describe)
-                    groups.matches()
-                    def major = groups.group(1)
-                    def minor = groups.group(2)
-                    def patch = groups.group(3)
-                    project.properties.release = major + "." + minor + "." + patch + "-SNAPSHOT"
-                  }
-                  catch (IllegalStateException e) {
-                    project.properties.release = ""
-                  }
-                }
-                else {
-                  // if we're building outside of Git, set a default
-                  // version number
-                  project.properties.release = project.properties.default
-                }
-                project.properties.shortrevision = ant.project.properties.shortrevision
-                project.properties.revision = ant.project.properties.revision
-
-                if (!project.properties.release) {
-                  // assume this is a source package outside of Git
-                  // there should be a ant/gitversion.xml file with the
-                  // version information used when the package was created
-
-                  def xmlfile = project.properties.get('project.rootdir') + "/ant/gitversion.xml"
-
-                  def xml = new XmlParser().parse(xmlfile)
-                  for (property in xml.property) {
-                    println "parsing " + property.'@name'
-                    if ('release.version' == property.'@name') {
-                      project.properties.release = property.'@value'
-                    }
-                    else if ('vcs.revision' == property.'@name') {
-                      project.properties.revision = property.'@value'
-                    }
-                    else if ('vcs.shortrevision' == property.'@name') {
-                      project.properties.shortrevision = property.'@value'
-                    }
-                  }
-                }
-
-                println "shortrevision = " + project.properties.shortrevision
-                println "revision = " + project.properties.revision
-                println "release = " + project.properties.release
-              </source>
-            </configuration>
-          </execution>
-        </executions>
-      </plugin>
 
       <!-- Add Implementation-Build entry to JAR manifest. -->
       <plugin>

ome-model_decoupling

#! /bin/bash

here=$(pwd)

# Initial clone
cd /tmp
rm -rf /tmp/bioformats || echo "Already cleaned"

# Clone Bio-Formats
git clone https://github.com/openmicroscopy/bioformats.git ome-model

# Filter branch to keep only the model components
cd ome-model
PATHS_TO_KEEP="cpp components/specification components/ome-xml components/xsd-fu CMakeLists.txt pom.xml .travis.yml docs/sphinx"
git filter-branch -f --index-filter "git rm --ignore-unmatch --cached -qr -- . && git reset -q \$GIT_COMMIT -- $PATHS_TO_KEEP" --prune-empty -- HEAD

# Clean empty commits
tmpfile=`mktemp -t splitgit`
chmod 755 $tmpfile
echo '#!/usr/bin/env ruby
old_parents = gets.chomp.gsub("-p ", " ")
new_parents = old_parents.empty? ? [] : `git show-branch --independent #{old_parents}`.split
puts new_parents.map{|p| "-p " + p}.join(" ")' > $tmpfile
git filter-branch -f --prune-empty --parent-filter $tmpfile HEAD
rm $tmpfile

# Apply git diff to let Travis compile
git apply $here/ome-model-diff